MmuINT0038962 @ mm10
Intron Retention
Gene
ENSMUSG00000032332 | Col12a1
Description
collagen, type XII, alpha 1 [Source:MGI Symbol;Acc:MGI:88448]
Coordinates
chr9:79656712-79657439:-
Coord C1 exon
chr9:79657300-79657439
Coord A exon
chr9:79656845-79657299
Coord C2 exon
chr9:79656712-79656844
Length
455 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACA
5' ss Score
8.1
3' ss Seq
ATTTTTCCTTTTTATCTAAGACC
3' ss Score
4.8
Exon sequences
Seq C1 exon
GGCGTGTTCCAGCCCCAACCAACCTCCAGTTTACTGAAGTCACACCAGAGAGTTTCAGGGGGACCTGGGATCATGGAGCTTCAGATGTGTCTCTCTACAGGATAACTTGGGCACCTGTTGGGAACCCAGATAAGATGGAG
Seq A exon
GTAACATTAGCTCTCTCCGTCTTTCCCTTCTGTCCCATTTTCTTTCTATTTGCTTATACGAAAGCCAGCAGACAGACATGGCAGCCAGAGCAGGAAGCTGGGAAGTCATGTCCTCAACTGCAAGCTAGGAGCAAATTAGAAGTGGAGCAAGGCTGTACACTCTTAAAGCCTACCTCTGTGATGTACTTCCTCCAGCAAGGCTTTACCTCCCTTTTGTCTCTCCAAACAGCACCAGCAAATGAGGACTGAGTATTCAAATCCCCGGGTCTATGACAGATTTCTTATTCAAAGCACCACCTTCCTTTAAAAAAAAATCATCTTTGACAAGTGGCTTCGGGCTCATGTACCTGTAGTGGTGCAGAAGAGCATTCACCTGTCAGCACAATGTTATTGGGGATGCGTCATCTAAATGGATATTAATTTAGTGTGCAAATGATTTTTCCTTTTTATCTAAG
Seq C2 exon
ACCATTTTAAATGGAGATGAAAATACTTTGGTGTTTGAAAATCTGAACCCCAATACTCCGTATGAAGTCTCCATCACCGCCATCTATCCTGATGAGTCTGAAAGCGAGGACCTGAGTGGCACAGAGCGCACAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032332:ENSMUST00000071750:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.426 A=NA C2=0.911
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.8=91.5)
A:
NA
C2:
PF0004116=fn3=PD(43.8=77.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTTCCAGCCCCAACCAAC
R:
GTGTGCGCTCTGTGCCAC
Band lengths:
270-725
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types